Research Article The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons) Rascha J. M. Nuijten, 1,2 Mirte Bosse, 1 Richard P. M. A. Crooijmans, 1 Ole Madsen, 1 Willem Schaftenaar, 3 Oliver A. Ryder, 4 Martien A. M. Groenen, 1 and Hendrik-Jan Megens 1 1 Animal Breeding and Genomics Centre (ABGC), Wageningen University, 6708 PB Wageningen, Netherlands 2 Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, Netherlands 3 Veterinary Services, Rotterdam Zoo, 3041 JG Rotterdam, Netherlands 4 San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA Correspondence should be addressed to Rascha J. M. Nuijten; rascha.nuijten@gmail.com Received 24 December 2015; Accepted 7 February 2016 Academic Editor: Cino Pertoldi Copyright © 2016 Rascha J. M. Nuijten et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Te list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Many endangered species are present in captivity and actively managed in breeding programs in which ofen little is known about the founder individuals. Recent developments in genetic research techniques have made it possible to sequence and study whole genomes. In this study we used the critically endangered Visayan warty pig (Sus cebifrons) as a case study to test the use of genomic information as a tool in conservation management. Two captive populations of S. cebifrons exist, which originated from two diferent Philippine islands. We found some evidence for a recent split between the two island populations; however all individuals that were sequenced show a similar demographic history. Evidence for both past and recent inbreeding indicated that the founders were at least to some extent related. Together with this, the low level of nucleotide diversity compared to other Sus species potentially poses a threat to the viability of the captive populations. In conclusion, genomic techniques answered some important questions about this critically endangered mammal and can be a valuable toolset to inform future conservation management in other species as well. 1. Introduction Te list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Current man- agement of endangered species includes in situ and ex situ measurements. In situ, that is, within the range of the species, most conservation actions focus on habitat protection (pro- tected areas), law enforcement (for reducing threats), and sometimes translocations or reintroductions [1]. For ex situ management, that is, outside the range of the species, such as in zoos or conservation centres, actions are mostly focused on keeping the population viable (both demographically and genetically) and as similar to the wild ancestor populations as possible (i.e., prevent adaptation to captivity [2]). Despite the successes achieved with these approaches, there are also several challenges, for example, in prioritizing species for conservation. In trying to solve this problem, the International Union for the Conservation of Nature (IUCN) in 1994 initiated a scientifc approach to categorise endangerment of species: the Red List of Treatened Species. Tis comprehensive list is currently a leading reference for governments, NGOs, and research institutions to decide on how to spend valuable resources for species conservation [1]. However, assessing a species properly is time-consuming and requires much information, which is ofen lacking. Additionally, not all species can be easily observed, creating a bias in the Red List towards the “easier observed” species [3]. If a species is not assessed well (or not assessed at all) the conservation actions planned for it might also miss their purpose. Another difculty is the time that is needed to assess a species, understand its situation, implement suitable conservation actions, and wait for them to have an efect. Hindawi Publishing Corporation International Journal of Genomics Volume 2016, Article ID 5613862, 9 pages http://dx.doi.org/10.1155/2016/5613862